Heat your oven to 375F. Line two baking pans with parchment paper.
Cut the Spaghetti Squash in half, lengthwise. Scoop out the seeds. Place both halves face down on one of the lined baking pans. Place this in the oven and bake for 30 - 40 minutes, until a knife inserted in the side proves that the spaghetti squash is tender.
Drain the can of beans. Place the beans in a food processor with the dehydrated onions, garlic powder, flax seeds, nutritional yeast flakes, Italian seasoning, and sage. Pulse until combined, only a few seconds. It should leave some pieces of the beans intact.
This makes a very sticky batter. You will want to use some kind of scoop (I used a cookie dough scooper) to create balls. Place the bean balls on the second parchment-lined pan. Place the bean meatballs in the oven, along side the spaghetti squash. Cook for 25 - 30 minutes.
Once the spaghetti squash is tender, remove from the oven and allow to cool for several minutes, until cool enough to handle. Place 3 - 4 paper towels on the counter. Then use a large spoon to scrape the spaghetti squash onto the paper towels. Squeeze the spaghetti squash a little to remove excess fluids.
Place the squeezed spaghetti squash into a casserole dish. Add the chia seeds and stir gently to distribute (these help soak up any extra liquids released from the spaghetti squash). Pour the spaghetti sauce on top.
Remove the pan of bean meatballs from the oven. Use tongs to transfer them on top of the spaghetti squash. Top with vegan mozzarella shreds. Return to the oven and bake another 10 minutes or so, until the cheese has melted.